MDM RNA-seq Analysis Report

Author

Antoine Chaillon

Published

1 December 2025

Note

RNAseq data from Adam Fields’ Laboratory, University of California San Diego (UCSD).

Summary

  • Number of samples: 2
  • Groups: HIV- moderate cannabis, HIV- daily cannabis, HIV- naive to cannabis, HIV+ naive to cannabis, HIV+ daily cannabis, HIV+ moderate cannabis
  • Treatments: CBD, CBDpIL1B, IL1B, THC, THCpIL1B, Vehicle
  • HIV status: HIVn, HIVp
  • Cannabis use: moderate, daily, naive

Workflow Overview

We processed the RNA-seq data from monocyte-derived macrophages (MDMs) using the following pipeline:

DESeq2 Model

The differential expression model used:

\[ design(dds) ~ treatment + HIV status + cannabis \]

  • treatment: vehicle, IL1b, CBD, THC, CBD+IL1B, THC+IL1b
  • hiv_status: HIV- vs HIV+
  • cannabis: naive, moderate, daily

Summary Analyses

Volcano Plots

volcano_list[["cannabis_daily_vs_naive"]]

PCA Plots

using ntop=500 top features by variance

using ntop=500 top features by variance

using ntop=500 top features by variance

using ntop=500 top features by variance

Top Genes Tables

DT::datatable(top20_list[["cannabis_daily_vs_naive"]], options = list(pageLength = 5, scrollX = TRUE), rownames = FALSE)
Note
  • Only genes with padj < 0.05 and |log2FC| > 1 are labeled in volcano plots.
  • PCA plots can be faceted by hiv_status to observe group separation.
  • Interactive tables allow scrolling and sorting top genes for each contrast.

HIV × Cannabis Interaction Analysis in MDMs

Methods

We computed per-donor log2 fold changes (log2FC) for each treatment contrast:

\[ \text{log2FC} = \log_2(\text{Treatment} + 1) - \log_2(\text{Control} + 1) \]

Contrasts included:

  • IL1B vs Vehicle
  • CBD+IL1B vs IL1B
  • THC+IL1B vs IL1B

Known inflammatory genes were highlighted to assess whether cannabis dampens IL1β-induced inflammation. For each gene and contrast, we fitted a linear model:

Next, we extracted the interaction terms to test whether cannabis use modulates IL1β-induced inflammation.

Top HIV × Cannabis interaction genes (ordered by raw p-value)

CBD and THC Modulation of IL1β Response (Key Inflammatory Genes)

  • Grey points: all other genes — context for overall variation.
  • Colored points + labels: known inflammatory genes (IL6, TNF, CXCL10, CCL2, NFKB1).
  • Y-axis (log2FC): positive → increased by cannabinoid, negative → decreased (potential dampening).
  • Black points and error bars: mean ± SD of inflammatory genes per cannabis group and HIV status.
  • Observation:
    • Most inflammatory genes are near 0, suggesting minimal average dampening by CBD or THC.
    • Some genes show donor-specific shifts, indicating variability among donors.
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